The first attempt to replace the wooden fort with a stone Kremlin was recorded in 1374, but construction was limited to a single tower, known as the Dmitrovskaya Tower (this has not survived). Under the rule of Ivan III, Nizhny Novgorod played the role of a guard city, having a permanent garrison; it served as a place for gathering troops for Moscow's actions against the Khanate of Kazan. In order to strengthen the defenses of the city, construction works on the walls began again.

Construction of the stone Kremlin of Nizhny Novgorod began in 1500 with the building of the Ivanovskaya Tower; the main work commenced in 1508 and by 1515 a grandiose building was completed. The oak walls that formed the old fortifications were destroyed by a huge fire in 1513. The two kilometer wall was reinforced by 13 towers (one of them - Zachatskaya - was on the shore of the Volga; not preserved, but was rebuilt in 2012). This "Stone City" had a permanent garrison with solid artillery weapons. With the fall of Kazan, Nizhny Novgorod Kremlin lost its military significance, and later it housed the city and provincial authorities.

The Council of Ministers of the RSFSR issued an order on January 30, 1949 for the restoration of the Nizhny Novgorod Kremlin